The coronavirus crisis has meant that scientific meetings and seminars have moved online. This change has led to me wondering: why don’t scientists give talks the way that musicians do gigs? The idea is: after posting a preprint or publishing a paper, a scientist advertises that they will livestream a seminar to explain the work. […]
Author: quantixed
Running Free: Calculating Efficiency Factor in R
Joe Friel reposted an article earlier this year on Efficiency Factor in running. Efficiency Factor (EF) can be viewed in Training Peaks software and he describes how it is calculated. This post describes how I went about calculating EF in R using a single gpx file. What is Efficiency Factor (EF)? Essentially, EF is the […]
Say It Ain’t So: using Weezer album cover colours in R
I’m a long-term fan of Weezer. Such was the brilliance of their first two albums that I have stuck with them through thick and thin. And dear me, there has been some very thin music. Nonetheless I own every album – thirteen of them. Among them are six albums entitled “Weezer”. These records are colloquially […]
Same Time Next Year: crunching PubMed data
I am giving a talk next week and wanted to update some plots from an old analysis that previously featured on quantixed. The question is: how long does it take for a paper get published? The answer is complex (as previously discussed on quantixed), but we can at least find out using data from PubMed […]
Screenager: screening times at bioRxiv
When a preprint is uploaded to bioRxiv, it undergoes screening before it appears online. How long does it take for Affiliates to screen preprints at bioRxiv? tl;dr I used R to look at bioRxiv screening times. Even though bioRxiv has expanded massively, screening happens quickly (in about 24 h). I am a bioRxiv Affiliate – […]
Take Off: preprints on COVID-19
I’m posting this the morning after generating a graph, and it’s already out-of-date. During the worldwide COVID-19 outbreak, preprint servers such as bioRxiv and medRxiv have again shown that they are the most effective way of communicating science rapidly. A collection of all papers on COVID-19 deposited on these two servers is available here, and […]
Find The Answer Within: using grep to find lost code
A short tech-tip this week. How can you find a line of code somewhere on your computer? I often find that I need to write a line of code and I can’t remember the exact syntax. To add to the frustration, I can remember writing a similar line before, but can’t remember in which file […]
Get Better: LaTeX and Overleaf
As part of the series on development of early career researchers in the lab, we spent a session (with homework) to learn how to write a document in LaTeX. Like the R session, we spent an hour or so in a room with laptops writing a document and then homework was set, to be completed for […]
On Steely Dan and lab management
As a scientist and a music lover, I see parallels in the process of doing science and in making music. They’re both creative endeavours after all. The lab’s latest paper is like an album release. The authors of the paper are like the players in the band. See, the analogy works quite well. So what […]
Get Better: R for absolute beginners
As part of the series on development of early career researchers in the lab, we spent three sessions over three weeks learning the basics of R. In my book “The Digital Cell”, I advocate R as the main number-crunching software but the R literacy in my lab is actually quite mixed. In order to know […]